Package de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper

Class Substance

java.lang.Object

de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.Substance

All Implemented Interfaces:

AttributeValuePairSupport, MappingDataEntity, SubstanceInterface, Cloneable, Comparable<SubstanceInterface>, Iterable<ConditionInterface>, Collection<ConditionInterface>, HelperClass

public class Substance
extends Object
implements SubstanceInterface, Cloneable

Field Summary

Fields

Modifier and Type	Field	Description
static boolean	includeEmptyAttributes

Fields inherited from interface de.ipk_gatersleben.ag_nw.graffiti.plugins.gui.editing_tools.script_helper.MappingDataEntity

ANNO_DIV

Constructor Summary

Constructors

Constructor	Description
Substance()
Substance(Map<?,?> map)

Method Summary

Modifier and Type	Method	Description
boolean	add(ConditionInterface e)
boolean	addAll(Collection<? extends ConditionInterface> c)
static void	addAndMerge(ExperimentInterface result, SubstanceInterface tobeMerged)
ConditionInterface	addAndMergeData(ConditionInterface seriesnew)
void	clear()
int	clearSynonyms()
SubstanceInterface	clone()
int	compareTo(SubstanceInterface o)
boolean	contains(Object o)
boolean	containsAll(Collection<?> c)
boolean	equals(Object obj)
void	fillAttributeMap(Map<String,Object> attributeValueMap)
String	getAffyHit()
static void	getAttributeString(StringBuilder s, String[] attributeNames, Object[] attributeValues)
static void	getAttributeString(StringBuilder s, String[] attributeNames, Object[] attributeValues, boolean asElements)
double	getAverage()
String	getClusterId()
Collection<ConditionInterface>	getConditions(Collection<String> validConditons)
int	getDataPointCount(boolean returnAvgValues)
Collection<MyComparableDataPoint>	getDataPoints(boolean returnAvgValues, boolean removeEmptyConditions)
String	getFormula()
String	getFuncat()
String	getInfo()
int	getMaximumSynonymeIndex(int returnIfNoSynonymes)
String	getName()
String	getNewBlast()
String	getNewBlastEval()
String	getNewBlastScore()
int	getNumberOfDifferentTimePoints()
String	getRowId()
String	getScore()
String	getSecure()
String	getSpot()
void	getStringOfChildren(StringBuilder s)
String	getSubstancegroup()
void	getSubstanceString(StringBuilder r)
double	getSum()
String	getSynonyme(int idx)
HashMap<Integer,String>	getSynonymMap()
Collection<String>	getSynonyms()
void	getXMLAttributeString(StringBuilder s)
String	getXMLstring()
int	hashCode()
boolean	isEmpty()
Iterator<ConditionInterface>	iterator()
boolean	remove(Object o)
boolean	removeAll(Collection<?> c)
boolean	retainAll(Collection<?> c)
void	setAffyHit(String affy_hit)
void	setAttribute(org.jdom2.Attribute attr)
void	setClusterId(String cluster_id)
boolean	setData(org.jdom2.Element experimentElement)
void	setDataOfChildElement(org.jdom2.Element childElement)
void	setDataOfChildElement(org.jdom2.Element childElement, org.jdom2.Element experimentChildElement)
void	setFormula(String formula)
void	setFuncat(String funcat)
void	setInfo(String info)
boolean	setMappedData(org.jdom2.Element e, org.jdom2.Element experimentChildElement)	Dataset, transformed for data mapping: <substance id="" name=""> <line experimentname="" genotype="WT" growthconditions="" id="1" name= "Unknown 1" treatment="" variety=""> <sample id="" measurementtool="" time="26" unit="day"> <average max="" min="" replicates="1" stddev="0.0" unit= "units">48.5313748658488</average> <data replicates="" unit="">48.5313748658488</data> </sample> ...
void	setName(String name)
void	setNewBlast(String new_blast)
void	setNewBlastEval(String new_blast_e_val)
void	setNewBlastScore(String new_blast_score)
void	setRowId(String rowId)
void	setScore(String score)
void	setSecure(String secure)
void	setSpot(String spot)
void	setSubstancegroup(String substancegroup)
void	setSynonyme(int idx, String value)
void	setSynonyme(HashMap<Integer,String> hashMap)
int	size()
Object[]	toArray()
<T> T[]	toArray(T[] a)
String	toString()
static void	validate(Document doc)

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Collection

parallelStream, removeIf, spliterator, stream, toArray

Methods inherited from interface java.lang.Iterable

forEach

Field Details

includeEmptyAttributes

public static boolean includeEmptyAttributes

Constructor Details

Substance

public Substance()

Substance

public Substance(Map<?,?> map)

Method Details

setMappedData

public boolean setMappedData(org.jdom2.Element e,
org.jdom2.Element experimentChildElement)

Dataset, transformed for data mapping: <substance id="" name=""> <line experimentname="" genotype="WT" growthconditions="" id="1" name= "Unknown 1" treatment="" variety=""> <sample id="" measurementtool="" time="26" unit="day"> <average max="" min="" replicates="1" stddev="0.0" unit= "units">48.5313748658488</average> <data replicates="" unit="">48.5313748658488</data> </sample> ...

Specified by:

setMappedData in interface SubstanceInterface

addAndMerge

public static void addAndMerge(ExperimentInterface result,
SubstanceInterface tobeMerged)

addAndMergeData

public ConditionInterface addAndMergeData(ConditionInterface seriesnew)

Specified by:

addAndMergeData in interface SubstanceInterface

getXMLstring

public String getXMLstring()

Specified by:

getXMLstring in interface SubstanceInterface

toString

public String toString()

Specified by:

toString in interface SubstanceInterface

Overrides:

toString in class Object

getXMLAttributeString

public void getXMLAttributeString(StringBuilder s)

Specified by:

getXMLAttributeString in interface MappingDataEntity

Specified by:

getXMLAttributeString in interface SubstanceInterface

getStringOfChildren

public void getStringOfChildren(StringBuilder s)

Specified by:

getStringOfChildren in interface MappingDataEntity

Specified by:

getStringOfChildren in interface SubstanceInterface

getAttributeString

public static void getAttributeString(StringBuilder s,
String[] attributeNames,
Object[] attributeValues)

getAttributeString

public static void getAttributeString(StringBuilder s,
String[] attributeNames,
Object[] attributeValues,
boolean asElements)

Parameters:

asElements - indicates, that the attribute shall be written as single element, eg
<attrname>attrvalue</attrname> instead attrname='attrvalue'

getDataPoints

public Collection<MyComparableDataPoint> getDataPoints(boolean returnAvgValues,
boolean removeEmptyConditions)

Specified by:

getDataPoints in interface SubstanceInterface

getSynonyms

public Collection<String> getSynonyms()

Specified by:

getSynonyms in interface SubstanceInterface

Returns:

Null or eventually empty list of synonyms.

getSynonymMap

public HashMap<Integer,String> getSynonymMap()

Specified by:

getSynonymMap in interface SubstanceInterface

getNumberOfDifferentTimePoints

public int getNumberOfDifferentTimePoints()

Specified by:

getNumberOfDifferentTimePoints in interface SubstanceInterface

clearSynonyms

public int clearSynonyms()

Specified by:

clearSynonyms in interface SubstanceInterface

setSynonyme

public void setSynonyme(int idx,
String value)

Specified by:

setSynonyme in interface SubstanceInterface

setSynonyme

public void setSynonyme(HashMap<Integer,String> hashMap)

Specified by:

setSynonyme in interface SubstanceInterface

getSynonyme

public String getSynonyme(int idx)

Specified by:

getSynonyme in interface SubstanceInterface

getFuncat

public String getFuncat()

Specified by:

getFuncat in interface SubstanceInterface

getInfo

public String getInfo()

Specified by:

getInfo in interface SubstanceInterface

getMaximumSynonymeIndex

public int getMaximumSynonymeIndex(int returnIfNoSynonymes)

Specified by:

getMaximumSynonymeIndex in interface SubstanceInterface

getAverage

public double getAverage()

Specified by:

getAverage in interface SubstanceInterface

setAttribute

public void setAttribute(org.jdom2.Attribute attr)

Specified by:

setAttribute in interface MappingDataEntity

Specified by:

setAttribute in interface SubstanceInterface

setData

public boolean setData(org.jdom2.Element experimentElement)

Specified by:

setData in interface MappingDataEntity

Specified by:

setData in interface SubstanceInterface

setDataOfChildElement

public void setDataOfChildElement(org.jdom2.Element childElement)

Specified by:

setDataOfChildElement in interface MappingDataEntity

Specified by:

setDataOfChildElement in interface SubstanceInterface

setDataOfChildElement

public void setDataOfChildElement(org.jdom2.Element childElement,
org.jdom2.Element experimentChildElement)

Specified by:

setDataOfChildElement in interface SubstanceInterface

getSubstanceString

public void getSubstanceString(StringBuilder r)

Specified by:

getSubstanceString in interface SubstanceInterface

compareTo

public int compareTo(SubstanceInterface o)

Specified by:

compareTo in interface Comparable<SubstanceInterface>

Specified by:

compareTo in interface SubstanceInterface

setRowId

public void setRowId(String rowId)

Specified by:

setRowId in interface SubstanceInterface

getRowId

public String getRowId()

Specified by:

getRowId in interface SubstanceInterface

setName

public void setName(String name)

Specified by:

setName in interface SubstanceInterface

getName

public String getName()

Specified by:

getName in interface SubstanceInterface

setFuncat

public void setFuncat(String funcat)

Specified by:

setFuncat in interface SubstanceInterface

setInfo

public void setInfo(String info)

Specified by:

setInfo in interface SubstanceInterface

setFormula

public void setFormula(String formula)

Specified by:

setFormula in interface SubstanceInterface

getFormula

public String getFormula()

Specified by:

getFormula in interface SubstanceInterface

setSubstancegroup

public void setSubstancegroup(String substancegroup)

Specified by:

setSubstancegroup in interface SubstanceInterface

getSubstancegroup

public String getSubstancegroup()

Specified by:

getSubstancegroup in interface SubstanceInterface

setClusterId

public void setClusterId(String cluster_id)

Specified by:

setClusterId in interface SubstanceInterface

getClusterId

public String getClusterId()

Specified by:

getClusterId in interface SubstanceInterface

setSpot

public void setSpot(String spot)

Specified by:

setSpot in interface SubstanceInterface

getSpot

public String getSpot()

Specified by:

getSpot in interface SubstanceInterface

setNewBlast

public void setNewBlast(String new_blast)

Specified by:

setNewBlast in interface SubstanceInterface

getNewBlast

public String getNewBlast()

Specified by:

getNewBlast in interface SubstanceInterface

setNewBlastEval

public void setNewBlastEval(String new_blast_e_val)

Specified by:

setNewBlastEval in interface SubstanceInterface

getNewBlastEval

public String getNewBlastEval()

Specified by:

getNewBlastEval in interface SubstanceInterface

setNewBlastScore

public void setNewBlastScore(String new_blast_score)

Specified by:

setNewBlastScore in interface SubstanceInterface

getNewBlastScore

public String getNewBlastScore()

Specified by:

getNewBlastScore in interface SubstanceInterface

setAffyHit

public void setAffyHit(String affy_hit)

Specified by:

setAffyHit in interface SubstanceInterface

getAffyHit

public String getAffyHit()

Specified by:

getAffyHit in interface SubstanceInterface

setScore

public void setScore(String score)

Specified by:

setScore in interface SubstanceInterface

getScore

public String getScore()

Specified by:

getScore in interface SubstanceInterface

setSecure

public void setSecure(String secure)

Specified by:

setSecure in interface SubstanceInterface

getSecure

public String getSecure()

Specified by:

getSecure in interface SubstanceInterface

validate

public static void validate(Document doc)
                     throws Exception

Throws:

Exception

getDataPointCount

public int getDataPointCount(boolean returnAvgValues)

Specified by:

getDataPointCount in interface SubstanceInterface

getSum

public double getSum()

Specified by:

getSum in interface SubstanceInterface

getConditions

public Collection<ConditionInterface> getConditions(Collection<String> validConditons)

Specified by:

getConditions in interface SubstanceInterface

add

public boolean add(ConditionInterface e)

Specified by:

add in interface Collection<ConditionInterface>

Specified by:

add in interface SubstanceInterface

iterator

public Iterator<ConditionInterface> iterator()

Specified by:

iterator in interface Collection<ConditionInterface>

Specified by:

iterator in interface Iterable<ConditionInterface>

Specified by:

iterator in interface SubstanceInterface

addAll

public boolean addAll(Collection<? extends ConditionInterface> c)

Specified by:

addAll in interface Collection<ConditionInterface>

Specified by:

addAll in interface SubstanceInterface

clear

public void clear()

Specified by:

clear in interface Collection<ConditionInterface>

Specified by:

clear in interface SubstanceInterface

contains

public boolean contains(Object o)

Specified by:

contains in interface Collection<ConditionInterface>

Specified by:

contains in interface SubstanceInterface

containsAll

public boolean containsAll(Collection<?> c)

Specified by:

containsAll in interface Collection<ConditionInterface>

Specified by:

containsAll in interface SubstanceInterface

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface Collection<ConditionInterface>

Specified by:

isEmpty in interface SubstanceInterface

remove

public boolean remove(Object o)

Specified by:

remove in interface Collection<ConditionInterface>

Specified by:

remove in interface SubstanceInterface

removeAll

public boolean removeAll(Collection<?> c)

Specified by:

removeAll in interface Collection<ConditionInterface>

Specified by:

removeAll in interface SubstanceInterface

retainAll

public boolean retainAll(Collection<?> c)

Specified by:

retainAll in interface Collection<ConditionInterface>

Specified by:

retainAll in interface SubstanceInterface

size

public int size()

Specified by:

size in interface Collection<ConditionInterface>

Specified by:

size in interface SubstanceInterface

toArray

public Object[] toArray()

Specified by:

toArray in interface Collection<ConditionInterface>

Specified by:

toArray in interface SubstanceInterface

toArray

public <T> T[] toArray(T[] a)

Specified by:

toArray in interface Collection<ConditionInterface>

Specified by:

toArray in interface SubstanceInterface

fillAttributeMap

public void fillAttributeMap(Map<String,Object> attributeValueMap)

Specified by:

fillAttributeMap in interface AttributeValuePairSupport

Specified by:

fillAttributeMap in interface SubstanceInterface

clone

public SubstanceInterface clone()

Specified by:

clone in interface SubstanceInterface

equals

public boolean equals(Object obj)

Specified by:

equals in interface Collection<ConditionInterface>

Overrides:

equals in class Object

hashCode

public int hashCode()

Specified by:

hashCode in interface Collection<ConditionInterface>

Overrides:

hashCode in class Object